tbuckley/cabot-search huggingface dataset:
Abstract 257: CDX model based genome-scale CRISPR KO screens for modulators of KRAS (G12C) inhibitor sensitivity
Authors: Haixin Zhao, Fangzheng Zhai, Bin Li, Qiangqiang Fan, Zhengang Peng
Journal: Cancer Research (2023)

Abstract KRAS is the most frequently mutated oncogene in human cancers and had long been considered an undruggable target for cancer therapy, until the FDA approval of Sotorasib (AMG 510) for the treatment of patients with non-small cell lung cancer (NSCLC) harboring the KRAS (G12C) mutation. To gain more insights into AMG 510 therapeutic mechanisms, herein we carried out a genome-scale CRISPR Cas9 knock-out screen in a KRAS G12C-harboring NCI-H2122 xenograft model. We first generated a stable NCI-H2122 cell line overexpressing Cas9 and confirmed its Cas9 editing efficiency by a BFP-GFP dual reporter system. Referring to our previous study for in vivo subcutaneous xenograft growth and response to AMG 510 treatment of NCI-H2122 cell line in immunodeficient mice, we decided to conduct the in vivo screens using 10M cell inoculation each mouse. We infected NCI-H2122 Cas9 cells with the genome-wide Brunello guide RNA library. After puromycin selection and two passages of cell recovery, the resultant cells were inoculated into Nu/nu mice subcutaneously, with part of cells collected as baseline. Mice bearing tumors were grouped into three groups at average tumor size of around 200 mm3 for vehicle, 10 or 30 mpk AMG510 treatment. Tumors were collected while the average tumor size of vehicle treatment group reached around 800 mm3. Genomic DNA was extracted from both baseline cell samples and tumor samples followed by Next-generation sequencing. We have performed QC analysis for all the samples and will discuss the hits from the screen and their implication in AMG 510-induced cancer sensitivity and resistance. Citation Format: Haixin Zhao, Fangzheng Zhai, Bin Li, Qiangqiang Fan, Zhengang Peng. CDX model based genome-scale CRISPR KO screens for modulators of KRAS (G12C) inhibitor sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 257.
Abstract 2435: Single cell spatial analysis identifies regulators of brain tumor initiating cells
Authors: Reza Mirzaei, Charlotte D’Mello, Marina Liu, Ana Nikolic, Mehul Kumar, Frank Visser, Pinaki Bose, Marco Gallo, Wee Yong
Journal: Cancer Research (2023)

Abstract Glioblastomas (GBMs) are aggressive brain tumors with extensive intratumoral heterogeneity. Here, we used spatial transcriptomics and single-cell ATAC-seq to dissect the transcriptome of distinct anatomical regions of the tumor microenvironment. We identified numerous extracellular matrix (ECM) molecules including biglycan elevated in areas infiltrated with brain tumor-initiating cells (BTICs). Single-cell RNA sequencing showed that the ECM molecules were differentially expressed by cells including injury response versus developmental BTICs. Exogeneous biglycan or overexpression of biglycan resulted in a higher proliferation rate of BTICs, and this was associated mechanistically with LDL receptor-related protein 6 (LRP6) binding and activation of the Wnt/β-catenin pathway. Biglycan-overexpressing BTICs grew to a larger tumor mass and higher mesenchymal phenotypes when implanted intracranially in mice. This study points to the spatial heterogeneity of ECM molecules in the GBM microenvironment and suggests biglycan-LRP6 axis as a therapeutic target to curb GBM growth. Citation Format: Reza Mirzaei, Charlotte D’Mello, Marina Liu, Ana Nikolic, Mehul Kumar, Frank Visser, Pinaki Bose, Marco Gallo, Wee Yong. Single cell spatial analysis identifies regulators of brain tumor initiating cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2435.
Abstract 342: Differential CD45 isoform expression and function in AML versus healthy leukocytes
Authors: Evan Ales, Robert Sackstein
Journal: Cancer Research (2023)

Abstract CD45 (the leukocyte common antigen) is a phosphatase present on all malignant and non-malignant leukocytes and hematopoietic progenitors and is the most abundant glycoprotein displayed by these cells. The human CD45 gene is alternatively spliced by reassortment of just three exons, exon 4 (“A”), exon 5 (“B”), and exon 6 (“C"), to create five distinct “R” isoforms (RO (no splice exons), RABC, RAB, RBC, and RB), with inclusion of A, B, or C exons enriching for expression of glycans (carbohydrates). Despite decades of investigation, the expression and phosphatase function of these isoforms on human AML cells remains unknown. To address this question, flow cytometry and western blot analysis was performed on AML primary cells (n=3) and KG1a and U937 cell lines versus healthy monocytes (n=3) utilizing exon-specific CD45-targetting mAbs. We then compared the contribution of CD45 phosphatase activity in KG1a and U937 cells versus healthy monocytes by employing a highly specific CD45 phosphatase inhibitor in cell culture for 24hrs, assessing induction of cell death after exposure to the inhibitor (n=3). Our results confirm reports of others indicating that "CD45RA- positivity" is a characteristic phenotype of AML cells, yet, distinctly, our data indicate that the most prevalent isoform identified on AML cells as "CD45RA-positive" is, actually, CD45RABC, the largest and most glycosylated isoform of CD45. This finding is in striking contrast to healthy monocytes, which do not express CD45RABC. Additionally, culturing of human AML cells with a CD45 phosphatase inhibitor induces rapid cell death within 24 hours but does not affect healthy monocytes. Thus, the conspicuous expression of the CD45 isoform CD45RABC among AML cells is associated with a survival advantage. Current studies in AML are directed to elaborating the prevalence of CD45RABC expression and uncovering the downstream effectors of its enzymatic activity to elucidate how such pathways sustain AML growth/survival. Citation Format: Evan Ales, Robert Sackstein. Differential CD45 isoform expression and function in AML versus healthy leukocytes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 342.
Abstract 1563: Concomitant inhibition of Aurora kinase A and WEE1 kinases results in synergistic tumor control and heightens DNA replication stress in head and neck and lung carcinomas
Authors: Jong Woo Lee, Sundong Kim, Sebastian Cruz-Gomez, Jackie Shi, Cindy Yang, Barbara Burtness
Journal: Cancer Research (2023)

Abstract Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) and lung cancer mainly harbor disruptive mutations in TP53 and/or CDKN2A tumor suppressor genes, which are associated with refractoriness to treatment as well as poor prognosis and survival. Mutational loss of TP53 function fosters elevated expression of Aurora kinase A (AURKA) that plays a crucial role in mitotic progression at G2/M and stabilizes DNA replication forks at S phase. We have previously demonstrated that combined inhibition of AURKA and WEE1, a G2/M checkpoint kinase induced by replication stress, results in synergistic anti-tumor effects in HNSCC in vitro and in vivo. We have now further confirmed synergy using the highly selective AURKA inhibitor VIC1911 in HNSCC and lung cancers harboring TP53 mutations and explored mechanisms of cell death. VIC1911 and adavosertib combination synergistically suppressed cell growth and survival in both 2D- and 3D-culture systems relative to vehicle or single-agent treatment in TP53-mutated HNSCC FaDu and CAL27, and lung cancer A549 and NCI-H358 cells, with no observable toxicity in normal cells, predicting a favorable therapeutic index. Furthermore, combination treatment accelerated mitotic entry and resulted in accumulation of mitotic catastrophe, as demonstrated by time-lapse imaging, and apoptotic cell death as evidenced by cleaved PARP assays. Notably, we found that combination VIC1911 and adavosertib in HNSCC cells drastically slowed and stalled progression of replication forks in DNA fiber analysis (Mean: DMSO=3.117; adavosertib=1.495; VIC1911=0.9757; combination=0.5548 kb/min; P &amp;lt;0.0001) and amplified DNA damage as measured by γH2AX, indicating induction of severe replication stress. In vivo, this combination resulted in significant tumor regression in both HNSCC and lung adenocarcinoma patient-derived and cancer cell-derived xenografted mice compared with either vehicle or single-agent treatment. Taken together, these results suggest that AURKA inhibition increases dependency on WEE1 by enhancing replication stress and mitotic catastrophe, and support clinical evaluation of combined AURKA and WEE1 inhibition as a novel and effective treatment for HNSCC and lung cancer patients with elevated AURKA expression. Citation Format: Jong Woo Lee, Sundong Kim, Sebastian Cruz-Gomez, Jackie Shi, Cindy Yang, Barbara Burtness. Concomitant inhibition of Aurora kinase A and WEE1 kinases results in synergistic tumor control and heightens DNA replication stress in head and neck and lung carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1563.
Abstract 2569: Investigation of the effect of chronic IL-1 exposure on breast cancer cell line response to external signaling factors
Authors: Roopal Dhar, Ola M. Olaleye, Rana Tarig Abdelaziz, Jyotsna Tera Reddy, Nikki Delk
Journal: Cancer Research (2023)

Abstract As part of our immune response, the body produces anti-tumorigenic inflammatory proteins to kill cancer cells. However, cancer cells can usurp chronic inflammation for their own survival. Interleukin-1 (IL-1) is an inflammatory protein found in breast cancer (BCa) tumors that is elevated in the BCa patient tumors and serum and promotes metastasis, indicating IL-1 is clinically relevant. But the molecular mechanisms underlying the effect of chronic IL-1 on BCa progression remain unknown. We previously discovered that acute exposure to IL-1 represses essential hormone receptors in cancers cells, but concomitantly upregulates other compensatory pro-survival proteins that contribute to tumor progression. To determine if chronic IL-1 inflammation has the same effect, we generated cell subline models using the human breast cancer cell line, T47D, by exposing T47D cells chronically to IL-1 for several months. Notably, we found that the T47D chronic IL-1 sublines stably evolve insensitivity to exogenous IL-1. This result suggests that chronic IL-1 causes stable molecular changes that may affect cancer cell response to exogenous factors.Therapeutic strategies include blocking exogenous hormone or growth factor signals in the tumor microenvironment to attenuate cancer cell growth, proliferation, and survival. Therefore, we grew T47D parental and chronic IL-1 sublines in the absence of serum to determine the effect of chronic IL-1 exposure on BCa cell response to hormone and growth factor inhibition. Preliminarily, we do not observe differences in parental versus subline response to serum starvation, suggesting that differential response to exogenous factors is specific to IL-1 signaling. To better understand how chronic IL-1 -induced molecular changes effect BCa cell response to the tumor microenvironment, we will perform sequencing and bioinformatics analysis to identify IL-1 -dependent and/or independent signaling pathways stably altered in the chronic IL-1 sublines. Citation Format: Roopal Dhar, Ola M. Olaleye, Rana Tarig Abdelaziz, Jyotsna Tera Reddy, Nikki Delk. Investigation of the effect of chronic IL-1 exposure on breast cancer cell line response to external signaling factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2569.
Abstract 2354: Regulation of TIMPs through MMP dependent cleavage in breast cancer
Authors: Sasha Coates-Park, Sadeechya Gurung, Josh Rich, William Stetler-Stevenson, David Peeney
Journal: Cancer Research (2023)

Abstract Tissue Inhibitors of Matrix Metalloproteinases (TIMPs) are a broadly expressed family of matrisome proteins that are the primary regulators of matrix metalloproteinases (MMPs). In addition to their originally described function, TIMPs display a broad range of MMP independent biological functions associated with proliferation, apoptosis, migration, and differentiation. MMPs are zinc containing endopeptidases that play an essential role in maintaining the extracellular matrix (ECM) through proteolytic turnover; a balancing act maintained (in part) by the local MMP:TIMP ratio. Disturbances in the balance between MMPs and TIMPs is associated with various disease states, including cancer, heart disease, arthritis, and cognitive dysfunction. While TIMPs are classically characterized as regulators of MMP proteolytic activity, we describe a novel mode of MMP-dependent regulation of TIMP function. We show that active MMP9 (aMMP9) in molar excess can cleave TIMP proteins within their C-terminal domains. As a result of this cleavage, the MMP-dependent and MMP-independent functions of the TIMP proteins are predicted to be altered. MMP9 has been found to contribute to the pathogenesis of many cancer types including breast cancer. Additionally, MMP9 is described as a breast cancer biomarker, with high levels of MMP9 being associated with a worse prognosis. Previous research from our lab has shown recombinant TIMP2 may represent a novel biological therapeutic in triple negative breast cancer models. Utilizing murine models of breast cancer, we describe the prevalence of TIMP cleavage in 4T1 breast tumors as well as the functional outcomes of TIMP cleavage within this model system. Studying the outcomes of TIMP regulation by MMPs may allow researchers to target this model system more effectively in translational studies of breast cancer. Citation Format: Sasha Coates-Park, Sadeechya Gurung, Josh Rich, William Stetler-Stevenson, David Peeney. Regulation of TIMPs through MMP dependent cleavage in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2354.
Abstract 6164: NF-κB and NRF2 signaling pathways affect prognosis in HPV-associated head and neck cancer
Authors: Aditi Kothari, Travis Parke Schrank, Wendell Gray Yarbrough, Natalia Isaeva
Journal: Cancer Research (2023)

Abstract Incidence of HPV associated head and neck squamous cell carcinoma (HNSCC) is on the rise, displaying a significantly favorable prognosis and overall better survival as compared to HPV negative HNSCC. Intense radiotherapy is the primary medical care leading to treatment associated morbidity in patients, thereby generating a need for de-intensification strategies. Biomarkers that can identify patients with less aggressive tumors as candidates for de-escalation therapy would revolutionize treatment. We applied an unbiased approach (weighted gene correlation network analysis (WGCNA)) that allows detection of autocorrelated gene sets on 3 independent cohorts of HPV+ HNSCC and created 22 consensus transcriptional modules by selecting genes that grouped together in WGCNA analyses from all 3 cohorts. Interestingly, only 1 module intrinsically divided HPV+ HNSCC into 2 subtypes, displaying different mutational profiles, mutational signatures, HPV gene expression patterns, HPV integration status, and patient survival. Gene set enrichment analysis revealed that this module was enriched in NF-kB genes and strongly associated with NF-κB signaling, confirming our prior findings that defined HPV+ HNSCC subtypes by presence or absence of NF-kB regulators, TRAF3 or CYLD defects and by the NF-κB activity classifier. Our studies show that NF- κB -driven intrinsic tumor characteristics contribute to increased sensitivity of NF- κB active HPV+ head and neck tumors to radiation, providing patients survival benefits. Indeed, TRAF3 or CYLD deletion activated NF-kB and dramatically increased radiation sensitivity of HPV+ head and neck cancer cells. In line with our RNA seq analysis, we found that activation of NF-κB via TRAF3/CYLD deletion significantly correlated with marked downregulation of NRF2 activity and reduced nuclear localization in in HPV+ HNSCC cells. Interestingly, TRAF3 CRISPR KO cells had lower NRF2 protein levels that were restored by MG132 treatment, indicating an involvement of KEAP1/CUL3 mediated proteasomal degradation of NRF2. In summary, our data unveils a unique relation between NF-κB pathway and radiosensitivity in HPV+ HNSCC. The distinct biological characteristics that separate patients into two subclasses associated with favorable prognosis could serve as a biomarker for personalized therapy. Citation Format: Aditi Kothari, Travis Parke Schrank, Wendell Gray Yarbrough, Natalia Isaeva. NF-κB and NRF2 signaling pathways affect prognosis in HPV-associated head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6164.
Abstract 258: Whole genome analysis of hereditary leiomyomatosis and renal cell cancer identifies role of localized hypermutational events
Authors: Selina Wu, Paul C. Boutros
Journal: Cancer Research (2023)

Abstract Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a rare hereditary condition affecting over 1 in 200,000 people worldwide. Individuals with HLRCC are also at risk of developing an aggressive form of renal cell carcinoma (RCC), as 15-20% of patients develop type 2 papillary RCC associated with poor prognosis. Although RCC risk and cancer penetrance of this condition has been studied, whole genome sequencing of associated tumors has yet to be examined, and the landscape of structural variants of HLRCC is largely unknown. We have therefore performed whole genome sequencing of tumor/normal pairs of HLRCC patients to study the tumor molecular architecture in this form of RCC. Through germline variant and somatic mutation calling, we have identified specific somatic mutational drivers, including those at the structural variant level for the first time in HLRCC. We have also quantified both chromothripsis and kataegis in these tumors, identifying the specific role of localized hypermutational events. Similarly, using tumour subclonal reconstruction techniques, we have inferred the clonality of HLRCC-associated RCC tumors and elucidate the relative timing of key oncogenic events and mutational processes. We also compare each of these mutational features to their equivalents in other RCC tumour subtypes. These studies shed key light on the specific mutational processes and drivers of this rare hereditary malignancy and on its lethality. Citation Format: Selina Wu, Paul C. Boutros. Whole genome analysis of hereditary leiomyomatosis and renal cell cancer identifies role of localized hypermutational events [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 258.
Abstract 487: ITI-1020, a novel PDE type 1 inhibitor, reduces tumor growth in triple negative breast cancer (TNBC) mouse models
Authors: Maud Voisin, Aksinija A. Kogan, Stephen Goding, Gretchen L. Snyder, Robert E. Davis
Journal: Cancer Research (2023)

Abstract Breast cancer is the most common cancer in women. Unfortunately, some patients do not benefit from most therapies and may even develop resistance to previously effective treatments leading to disease progression. Therefore, treatment resistance remains a significant challenge and new treatments are needed to overcome this problem. ITI-1020 is a potent and highly selective inhibitor of the phosphodiesterase 1 (PDE1) enzyme. Given the role of PDE1 in the regulation of essential cellular functions, including among others the transition of monocytes to macrophages and potentially the infiltration of macrophages into the tumor microenvironment (TME), we hypothesize that ITI-1020 will alter macrophage infiltration and polarization, as well as improve T cell function and recruitment into the TME, thereby promoting antitumor immunity in murine cancer models. We tested this hypothesis by studying the effect of ITI-1020 given, alone or in combination a PD-1 immune checkpoint inhibitor, on tumor growth, and TME composition of E0771 and 4T1 tumor-bearing mice, two syngeneic models of TNBC. Mice treated with ITI-1020 alone or in combination with anti-PD-1 antibody showed significant inhibition of tumor growth compared to isotype controls in both type of tumors. Flow cytometry analysis of the tumor microenvironment showed a significant shift in the polarization of macrophages toward a more inflammatory phenotype, and/or a reduction in the number of exhausted T cells. Furthermore, scRNAseq analysis of tumors from mice treated with ITI-1020 in monotherapy showed altered expression of genes involved in inflammatory processes and cell proliferation within the tumor microenvironment and in the cancer cells. These results suggest that ITI-1020 promotes antitumor immunity by a novel mechanism (PDE1 inhibition), leading to tumor growth inhibition in E0771 and 4T1 tumor models. Translating these findings to the clinic may provide a new hope for the treatment of refractory or resistant TNBC tumors. Citation Format: Maud Voisin, Aksinija A. Kogan, Stephen Goding, Gretchen L. Snyder, Robert E. Davis. ITI-1020, a novel PDE type 1 inhibitor, reduces tumor growth in triple negative breast cancer (TNBC) mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 487.